Micro-machining of low-to-high aspect ratio (depth/width) microchannels has numerous applications in biomedical, micro-electromechanical, and microfluidic systems. Milling micro-features in advanced engineering materials (AEMs) using a conventional micro-machining route is challenging. Specifically, generating a controlled freeform surface with acceptable dimensional tolerance in Ti-alloys is difficult. The necessity to machine a wide range of ductile-behaving AEMs (with minimal residual stress, no heat-affected zone, and relatively minor edge damage) demands alternative technologies. The present study employed micro-abrasive waterjet (μ-AWJ) technology to perform controlled-depth milling of low-to-high aspect ratio microchannels without masking the Ti-6Al-4V target. In addition, a hybrid model is proposed to predict the cross-section profiles (CPs) of the microchannels milled in linear jet pass erosion. The hybrid model includes two modules: (i) high-energy jet flow dynamics—which outputs the particle flow properties in the jet plume, and (ii) a normal jet-impinged erosion—which predicts the microchannel CPs. Experimentally milled microchannels in single jet pass erosion have an aspect ratio of 0.06–0.19. Model results show that the prediction error in microchannel erosion depth is < 1%, and their CPs with a maximum mean absolute error of < 9.4 μm. A strong conformity is observed between the experimentally generated CPs and model-predicted ones, with a correlation coefficient 0.98. Overall, the study demonstrated the accurate prediction of microchannel CPs using a proposed hybrid model—one of the building blocks. Thus, the model aids in manufacturing a desired microchannel geometry generated by μ-AWJs and serves as an initial step to building freeform surface modules.